From 964771c5f22654413bd31d0fcddb5846d456b51f Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
Date: Tue, 20 Dec 2022 17:33:04 +0100
Subject: [PATCH] Update docs/output.md

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
---
 docs/output.md | 23 +++++++++++++++--------
 1 file changed, 15 insertions(+), 8 deletions(-)

diff --git a/docs/output.md b/docs/output.md
index b9a7a64..12a4194 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -209,20 +209,27 @@ You will only recieve the FASTQs and `*classifiedreads.txt` file if you supply `
 
 ### KrakenUniq
 
+[KrakenUniq](https://github.com/fbreitwieser/krakenuniq) (formerly KrakenHLL) is an extenson to the fast k-mer-based classification [Kraken](https://github.com/DerrickWood/kraken) with an efficient algorithm for additionally assessing the coverage of unique k-mers found in each species in a dataset.
+
 <details markdown="1">
 <summary>Output files</summary>
 
-- `krakenuniq`
-
-  - `<sample_id>.classified.fastq.gz`
-  - `<sample_id>.krakenuniq.classified.txt`
-  - `<sample_id>.krakenuniq.report.txt`
-  - `<sample_id>.unclassified.fastq.gz`
-
-  ## interleaved?
+- `krakenuniq/`
+  - <db_name>/
+    - `<sample_id>_<db_name>.classified.fastq.gz`: FASTQ file containing all reads that had a hit against a reference in the database for a given sample
+    - `<sample_id>_<db_name>.unclassified.fastq.gz`: FASTQ file containing all reads that did not have a hit in the database for a given sample
+    - `<sample_id>_<db_name>.report.txt`: A Kraken2-style report that summarises the fraction abundance, taxonomic ID, number of Kmers, taxonomic path of all the hits, with an additional column for k-mer coverage, that allows for more accurate distinguishing between false-positive/true-postitive hits
+    - `<sample_id>_<db_name>.classifiedreads.txt`: A list of read IDs and the hits each read had against each database for a given sample
 
 </details>
 
+The main taxonomic profiling file from KrakenUniq is the `*report.txt` file. This is an extension of the Kraken2 report with the additional k-mer coverage information that provides more information about the accuracy of hits.
+
+> ⚠️ The output system of KrakenUniq can result in other `stdout` or `stderr` logging information being saved in the report file, therefore you must check your report files before downstream use!
+
+You will only receive the FASTQs and `*classifiedreads.txt` file if you supply `--krakenuniq_save_reads` and/or `--krakenuniq_save_readclassification` parameters to the pipeline.
+
+
 ### Centrifuge
 
 <details markdown="1">